Just an update to the question you asked before. I successfully transferred my linked tree to another computer, worked on it there, transferred it back to the original machine, and then successfully synchronized. On top of that, the computer to which I transferred it did not have an updated version of FTM 2012, but that didn't seem to make a difference.
I no longer make .ftmb files. I just run the script I created which copies all of my files and folders in a compressed archive to another drive. It took me about an hour to write the script. Not sure what's taking Ancestry so long to release an update that allows for linked trees to be backed up and restored.